Hi, Sorry for the delay, I just came back from a 2 week holiday. This is correct, the func_mf, func_local_tm, etc. methods are working on a single spin. This is stored in self.data[0]. The other functions work on multiple spin data located in self.data[0], self.data[1], etc.
Regards, Edward On 14 October 2010 19:38, Pavel Kaderavek <pavel.kadera...@gmail.com> wrote: > Hi, > > I would like to announce a small clarification of my previous mail about > changes in functions func_mf, func_local_tm, func_diff, func_all, and their > derivatives (class Mf, file maths_fns/mf.py). Loop suggested in my last > post: > > https://mail.gna.org/public/relax-devel/2010-09/msg00020.html > > is valid just for the functions func_diff, func_all, and their equivalents > for a first and second derivatives. > While for the functions func_mf, func_local_tm, and corresponding > derivatives the index of self.num_interactions should be set to `0` instead > of index `i` > > for j in xrange(self.num_interactions[0]): > > (The rest of the loop remains the same) > That comes from the fact that these functions (func_mf, func_local_tm, ... > ) are called for each spin separately. As it is indicated by the preceding > statement: > > data = self.data[0] > > Regards, > Pavel > > On 29 September 2010 10:53, Edward d'Auvergne <edw...@nmr-relax.com> wrote: >> >> Hi, >> >> This is the perfect approach. It will abstract the calculations so >> that we will not need to touch many of maths_fns modules. With this >> code in place, I would aim at then making the test suite pass again by >> having the correct data structures pass into maths_fns.mf. The last >> step would be to input CSA tensors and the multi-dipole interactions >> via user functions. If you make a patch for all of the func_*(), >> dfunc_*(), and d2func_*() methods, I can check and apply it quickly. >> >> Regards, >> >> Edward >> >> >> On 28 September 2010 12:07, Pavel Kaderavek <pavel.kadera...@gmail.com> >> wrote: >> > Hi, >> > we were thinking about next necessary changes in the CST branch. >> > >> > Now we need to break through the problem, which implies the fact we >> > split >> > the relaxation rate calculation into contributions of individual >> > interactions. Each of them has its own data class to store its >> > parameters >> > (so far called data[i][j], where the [i] was a spin index and [j] was >> > the >> > interaction index). >> > >> > It seems to us, that it the best way to deal with it is to edit >> > functions: >> > func_mf, func_local_tm , func_diff, func_all and their equivalents for a >> > first and second derivatives (defined in mf.py file). >> > >> > Within these functions the calculations of direction cosines, diffusion >> > tensor weight calculations, components of the spectral densities and so >> > on >> > are performed. All these must be calculated for each interaction >> > separately, >> > because each interaction has its own data storage (which replaced >> > previously >> > used one data class container for the whole IS spin system). >> > >> > Instead of: >> > >> > >> > # Direction cosine calculations. >> > if self.diff_data.calc_di: >> > self.diff_data.calc_di(data, self.diff_data) >> > >> > # Diffusion tensor weight calculations. >> > self.diff_data.calc_ci(data, self.diff_data) >> > >> > # Diffusion tensor correlation times. >> > self.diff_data.calc_ti(data, self.diff_data) >> > >> > # Calculate the components of the spectral densities. >> > if data.calc_jw_comps: >> > data.calc_jw_comps(data, params) >> > >> > # Calculate the R1, R2, and sigma_noe values. >> > data.ri_prime = data.create_ri_prime(data) >> > >> > >> > we would suggest to introduce a loop over interacations >> > for j in xrange(self.num_interactions[i]): >> > # Direction cosine calculations. >> > if self.diff_data.calc_di: >> > self.diff_data.calc_di(data[j], self.diff_data) >> > >> > # Diffusion tensor weight calculations. >> > self.diff_data.calc_ci(data[j], self.diff_data) >> > >> > # Diffusion tensor correlation times. >> > self.diff_data.calc_ti(data[j], self.diff_data) >> > >> > # Calculate the components of the spectral densities. >> > if data.calc_jw_comps: >> > data.calc_jw_comps(data[j], params) >> > >> > # Calculate the R1, R2, and sigma_noe components. >> > data.ri_prime = data.create_ri_prime(data[j]) >> > >> > >> > It must be accompanied in the next step by a change the ri_prime >> > function so >> > that it just calculate only a product of specific interaction constant >> > and >> > corresponding linear combination of spectral densities. While the final >> > sumation over all interactions should be done in a separate step. >> > >> > Moreover it will be also necessary to distinguish within the function >> > setup_equation the type of equation used for contribution of individual >> > interactions according to their type. >> > >> > Best >> > Pavel >> > >> > >> > On 10 September 2010 15:43, Edward d'Auvergne <edw...@nmr-relax.com> >> > wrote: >> >> >> >> Hi Pavel, >> >> >> >> I missed it in the patches, but there were tab characters '\t' causing >> >> problems. These are now fixed. relax requires that a tab is replaced >> >> by 4 spaces. I have also added you to the copyright notices >> >> (http://svn.gna.org/viewcvs/relax?view=rev&revision=11543) of the >> >> files you have modified. >> >> >> >> Regards, >> >> >> >> Edward >> >> >> >> On 10 September 2010 15:36, Edward d'Auvergne <edw...@nmr-relax.com> >> >> wrote: >> >> > Hi, >> >> > >> >> > I've carefully checked the patches and committed them with the >> >> > messages you wrote. Sorry again for the delays. It should be faster >> >> > now that I am no longer in the tropical wilderness of far north >> >> > Australia. >> >> > >> >> > Regards, >> >> > >> >> > Edward >> >> > >> >> > >> >> > On 6 September 2010 13:23, Edward d'Auvergne <edw...@nmr-relax.com> >> >> > wrote: >> >> >> Hi Pavel, >> >> >> >> >> >> Sorry for the delayed response. I was at the ICMRBS conference in >> >> >> Australia and then travelled through the tropical north end of >> >> >> Australia afterwards. I came back yesterday out of the remote >> >> >> wilderness and can soon start looking at this patches. >> >> >> >> >> >> Regards, >> >> >> >> >> >> Edward >> >> >> >> >> >> >> >> >> On 31 August 2010 18:00, Pavel Kaderavek <pavel.kadera...@gmail.com> >> >> >> wrote: >> >> >>> Hi, >> >> >>> >> >> >>> some time ago, we submitted two patches regarding CST branch. We >> >> >>> are >> >> >>> not >> >> >>> sure if we should wait for some additional comment from your side, >> >> >>> or >> >> >>> we can >> >> >>> continue with introducing further changes in the code. >> >> >>> Next step would be a splitting of the relaxation equation so that >> >> >>> contribution to the relaxation due to the individual types of >> >> >>> interaction >> >> >>> (dipole-dipole, CSA) can be calculated separately. >> >> >>> >> >> >>> >> >> >>> Regars, >> >> >>> >> >> >>> Pavel, Petr >> >> >>> >> >> >> >> >> > >> > >> > > > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
